1
|
Nguyen SV, Escobar VH, Ali SS, Puthuveetil NP, Petrone JR, Kirkland JL, Gaffney K, Tabron CL, Wax N, Duncan J, King S, Marlow R, Reese AL, Yarmosh DA, McConnell HH, Fernandes AS, Bagnoli J, Benton B, Jacobs JL. Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov. Int J Syst Evol Microbiol 2025; 75. [PMID: 40397495 DOI: 10.1099/ijsem.0.006797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025] Open
Abstract
Whole-genome sequencing of cultures at the American Type Culture Collection (ATCC®) is ongoing, with reference-quality genome sequences for our microbial strains added to the ATCC® Genome Portal on a quarterly basis. Following genome assembly, authentication and taxonomy verification are needed for taxonomic updates based on the circumscription of genomic metrics for a species. Moraxella sp. ATCC 23246T was originally identified as an atypical Moraxella catarrhalis; however, an analysis of the complete and closed genome of this strain indicates that it represents a novel species within the Moraxella genus. We propose the name of Moraxella veridica sp. nov. for this long-mischaracterized strain as whole-genome sequencing was used to uncover the truth of this strain's identity. The type strain is ATCC 23246T (=NCTC 4103T).
Collapse
|
2
|
Taoka M, Kuwana R, Murakami Y, Kashima A, Nobe Y, Uekita T, Takamatsu H, Ichimura T. The ionic liquid-assisted sample preparation method pTRUST allows sensitive proteome characterization of a variety of bacterial endospores to aid in the search for protein biomarkers. PLoS One 2025; 20:e0318186. [PMID: 39854521 PMCID: PMC11760639 DOI: 10.1371/journal.pone.0318186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 01/11/2025] [Indexed: 01/26/2025] Open
Abstract
Bacterial endospores are ubiquitous and are responsible for various human infections. Recently, we reported that an ionic liquid (IL)-based sample preparation method (named pTRUST) facilitated highly efficient shotgun analysis of the Bacillus subtilis spore proteome in trace samples. In this study, we evaluated the efficiency and applicability of the pTRUST technology using three different spore preparations: one purified from the closely related subspecies B. subtilis natto and two from B. licheniformis and B. cereus. We showed that the pTRUST method allowed rapid solubilization and processing of all tested spore samples prepared for highly sensitive mass spectrometry (MS) analysis. Bioinformatics analysis using the BLAST program suggested that a set of 25 proteins commonly identified between the above three species and B. subtilis spores may be universal biomarkers among various bacterial species, including 43 spore-producing bacteria associated with industrial dairy processing environments and product spoilage. In contrast, the two identified proteins, D4FV94 in B. subtilis natto and Q737A2 in B. cereus, are likely species-specific biomarkers, because their orthologs are absent or rare in all organisms. The sensitivity and applicability of pTRUST, along with the putative protein biomarkers identified in this study, will facilitate a wide spectrum of spore research for biological and clinical applications.
Collapse
Affiliation(s)
- Masato Taoka
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Ritsuko Kuwana
- Faculty of Pharmaceutical Science, Setsunan University, Osaka, Japan
| | - Yoshinari Murakami
- Department of Applied Chemistry, National Defense Academy, Kanagawa, Japan
| | | | - Yuko Nobe
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Takamasa Uekita
- Department of Applied Chemistry, National Defense Academy, Kanagawa, Japan
| | - Hiromu Takamatsu
- Faculty of Pharmaceutical Science, Setsunan University, Osaka, Japan
| | - Tohru Ichimura
- Department of Applied Chemistry, National Defense Academy, Kanagawa, Japan
| |
Collapse
|
3
|
Magome TG, Ochai SO, Hassim A, Bezuidenhout CC, van Heerden H, Lekota KE. A genome-based investigation of the Priestia species isolated from anthrax endemic regions in Kruger National Park. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105649. [PMID: 39059732 DOI: 10.1016/j.meegid.2024.105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Priestia is a genus that was renamed from the genus Bacillus based on the conserved signature indels (CSIs) in protein sequences that separate Priestia species from Bacillus, with the latter only including species closely related to B. subtilis and B. cereus. Diagnosis of anthrax, a zoonotic disease, is implicated by tripartite anthrax virulence genes (lef, pagA, and cya) and poly-γ-D-glutamic acid capsular genes cap-ABCDE of Bacillus anthracis. Due to the amplification of anthrax virulence genes in Priestia isolates, the search for homologous anthrax virulence genes within the Priestia genomes (n = 9) isolated from animal blood smears was embarked upon through whole genome sequencing. In silico taxonomic identification of the isolates was conducted using genome taxonomy database (GTDB), average nucleotide identity (ANI), and multi-locus sequence typing (MLST), which identified the genomes as P. aryabhattai (n = 5), P. endophytica (n = 2) and P. megaterium (n = 2). A pan-genome analysis was further conducted on the Priestia genomes, including the screening of virulence, antibiotic resistance genes and mobile genetic elements on the sequenced genomes. The oligoribonuclease NrnB protein sequences showed that Priestia spp. possess a unique CSI that is absent in other Bacillus species. Furthermore, the CSI in P. endophytica is unique from other Priestia spp. Pan-genomic analysis indicates that P. endophytica clusters separately from P. aryabhattai and P. megaterium. In silico BLASTn genome analysis using the SYBR primers, Taqman probes and primers that target the chromosomal marker (Ba-1), protective antigen (pagA), and lethal factor (lef) on B. anthracis, showed partial binding to Priestia regions encoding for hypothetical proteins, pyridoxine biosynthesis, hydrolase, and inhibitory proteins. The antibiotic resistance genes (ARG) profile of Priestia spp. showed that the genomes contained no more than two ARGs. This included genes conferring resistance to rifamycin and fosfomycin on P. endophytica, as well as clindamycin on P. aryabhattai and P. megaterium. Priestia genomes lacked B. anthracis plasmids and consisted of plasmid replicon types with unknown functions. Furthermore, the amplification of Priestia strains may result in false positives when qPCR is used to detect the virulence genes of B. anthracis in soil, blood smears, and/or environmental samples.
Collapse
Affiliation(s)
- Thuto Gomolemo Magome
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom, South Africa.
| | - Sunday Ochonu Ochai
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa; International Centre for Antimicrobial Resistance Solutions, Copenhagen S, 2300, Denmark; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | | | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Kgaugelo Edward Lekota
- Unit for Environmental Sciences and Management, Microbiology, North-West University, Potchefstroom, South Africa
| |
Collapse
|
4
|
Bielen A, Babić I, Vuk Surjan M, Kazazić S, Šimatović A, Lajtner J, Udiković-Kolić N, Mesić Z, Hudina S. Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21752-21764. [PMID: 38393570 DOI: 10.1007/s11356-024-32537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
Collapse
Affiliation(s)
- Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
| | - Ivana Babić
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Marija Vuk Surjan
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Ana Šimatović
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Jasna Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Zrinka Mesić
- Oikon Ltd., Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| |
Collapse
|
5
|
M N, G S S, J S, K H, C S, P M, R N, C P S, N C, Ram B, C A, B S. Whole genome analysis and functional characterization of a novel Bacillus thuringiensis (Bt 62) isolate against sugarcane white grub Holotrichia serrata (F). Genomics 2021; 114:185-195. [PMID: 34933070 DOI: 10.1016/j.ygeno.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/18/2021] [Accepted: 12/15/2021] [Indexed: 11/19/2022]
Abstract
In this study, we report the whole genome assembly of Bt 62, a novel isolate harbouring cry8 holotype gene identified by us earlier. Sequencing was carried out using a combination of Illumina NextSeq 500 and Oxford Nanopore sequencing Technologies (ONT). The final assembled genome was 6.13 Mb comprising a circular chromosome and four plasmids. The bioassay studies against Holotrichia serrata (F.) (Coleoptera: Scarabaeidae), a polyphagous pest infesting sugarcane and other crops, indicated significant toxicity to first instar grubs over untreated larvae achieving a highest mean mortality of 91.11% for various doses tested. In vitro proteolytic assay and histopathological studies of the midgut of infected white grubs revealed proteolytic processing of the protoxin and extensive degeneration of larval midgut epithelial cells. The results demonstrate that this novel isolate could be used as a biopesticide or its crystal toxin genes could be expressed in sugarcane and other crops for resistance against H. serrata.
Collapse
Affiliation(s)
- Naveenarani M
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Suresha G S
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Srikanth J
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Hari K
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Sankaranarayanan C
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Mahesh P
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Nirmala R
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Swathik C P
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Crickmore N
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Bakshi Ram
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Appunu C
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India
| | - Singaravelu B
- ICAR- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India.
| |
Collapse
|
6
|
Shikov AE, Malovichko YV, Lobov AA, Belousova ME, Nizhnikov AA, Antonets KS. The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis. Int J Mol Sci 2021; 22:2244. [PMID: 33668147 PMCID: PMC7956386 DOI: 10.3390/ijms22052244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Bacillus thuringiensis, commonly referred to as Bt, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make Bt a prominent source of biologicals. To categorize the exuberance of Bt strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of Bt strains' phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in Bt strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of Bt culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the israelensis-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the israelensis strain were also compared to the spores of strains belonging to two other major Bt serovars, namely darmstadiensis and thuringiensis. The identified proteins were analyzed regarding the presence of the respective genes in the 104 Bt genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains' phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains.
Collapse
Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Arseniy A. Lobov
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
- Laboratory of Regenerative Biomedicine, Institute of Cytology of the Russian Academy of Science, 194064 St. Petersburg, Russia
| | - Maria E. Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| |
Collapse
|
7
|
Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
Collapse
Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
| |
Collapse
|
8
|
Isolation and Molecular Characterization of Antibiotic Producing Bacillus licheniformis Strains Isolated from Soil. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.4.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Currently, there is an increase prevalence of antibiotic-resistant bacteria worldwide. Therefore, the need for characterization of naturally occuring antibiotics with less antibiotic resistance is required. Soil resources contains valuable antibiotic producing microorganisms that increasingly being utilized for the production of suitable antibiotics. Therefore, this study aimed at identifying an antibiotic bacteria with ability of producing antibiotic that is isolated from soil samples collected from Al Zarqa provenance, an arid area in Jordan. Morphological and biochemical characterization of the isolates were carried out and found that all of the isolates belong to Bacillus genus. Further confirmation of the characterization of the bacteria was done by ribosomal RNA and PCR. The results reveal that the isolates represent Basilluslicheniformis. These bacilli were further investigated for antimicrobial activities against 6 ATCC human pathogens viz., S. aureus, S. pneumonia, Salmonella typhi., E. coli, P. mirabels and E. cloacae. Additionally, the results of Gas Chromatography Mass Spectrometry (GCMS) of ethyl acetate extracts for B. licheniformis secondary metabolites showed that they contain two main antimicrobial compounds namely Pyrrolo [1, 2-a] pyrazine-1, 4-dione,hexahydro and Trans-13-octadecenoic acid. The present work maybe suggests that soil isolates from the studied arid area include antibiotic producing strains that can be utilized commercially.
Collapse
|
9
|
Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
Collapse
Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| |
Collapse
|
10
|
Borrayo E, May-Canche I, Paredes O, Morales JA, Romo-Vázquez R, Vélez-Pérez H. Whole-Genome k-mer Topic Modeling AssociatesBacterial Families. Genes (Basel) 2020; 11:genes11020197. [PMID: 32075081 PMCID: PMC7074292 DOI: 10.3390/genes11020197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 11/16/2022] Open
Abstract
Alignment-free k-mer-based algorithms in whole genome sequence comparisons remainan ongoing challenge. Here, we explore the possibility to use Topic Modeling for organismwhole-genome comparisons. We analyzed 30 complete genomes from three bacterial families bytopic modeling. For this, each genome was considered as a document and 13-mer nucleotiderepresentations as words. Latent Dirichlet allocation was used as the probabilistic modeling of thecorpus. We where able to identify the topic distribution among analyzed genomes, which is highlyconsistent with traditional hierarchical classification. It is possible that topic modeling may be appliedto establish relationships between genome's composition and biological phenomena.
Collapse
Affiliation(s)
- Ernesto Borrayo
- Electronics Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico;
| | - Isaias May-Canche
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico; (I.M.-C.); (O.P.); (J.A.M.); (R.R.-V.)
- Instituto Tecnológico de Chetumal, Quintana Roo 77000, Mexico
| | - Omar Paredes
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico; (I.M.-C.); (O.P.); (J.A.M.); (R.R.-V.)
| | - J. Alejandro Morales
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico; (I.M.-C.); (O.P.); (J.A.M.); (R.R.-V.)
| | - Rebeca Romo-Vázquez
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico; (I.M.-C.); (O.P.); (J.A.M.); (R.R.-V.)
| | - Hugo Vélez-Pérez
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Jalisco 44100, Mexico; (I.M.-C.); (O.P.); (J.A.M.); (R.R.-V.)
- Correspondence:
| |
Collapse
|
11
|
Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, Malorny B. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog 2019; 11:48. [PMID: 31636715 PMCID: PMC6791114 DOI: 10.1186/s13099-019-0330-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.
Collapse
Affiliation(s)
- Laura Uelze
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Cécile Jacobs
- Landeslabor Schleswig-Holstein, Max-Eyth-Straße 5, 24537 Neumünster, Germany
| | - István Szabó
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| |
Collapse
|
12
|
Pornsukarom S, van Vliet AHM, Thakur S. Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources. BMC Genomics 2018; 19:801. [PMID: 30400810 PMCID: PMC6218967 DOI: 10.1186/s12864-018-5137-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states. Results WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples. Conclusions WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars. Electronic supplementary material The online version of this article (10.1186/s12864-018-5137-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Suchawan Pornsukarom
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi, Thailand
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
13
|
Interaction between Insects, Toxins, and Bacteria: Have We Been Wrong So Far? Toxins (Basel) 2018; 10:toxins10070281. [PMID: 29986377 PMCID: PMC6070883 DOI: 10.3390/toxins10070281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/01/2018] [Accepted: 07/02/2018] [Indexed: 12/19/2022] Open
Abstract
Toxins are a major virulence factor produced by many pathogenic bacteria. In vertebrates, the response of hosts to the bacteria is inseparable from the response to the toxins, allowing a comprehensive understanding of this tripartite host-pathogen-toxin interaction. However, in invertebrates, this interaction has been investigated by two complementary but historically distinct fields of research: toxinology and immunology. In this article, I highlight how such dichotomy between these two fields led to a biased, or even erroneous view of the ecology and evolution of the interaction between insects, toxins, and bacteria. I focus on the reason behind such a dichotomy, on how to bridge the fields together, and on confounding effects that could bias the outcome of the experiments. Finally, I raise four questions at the border of the two fields on the cross-effects between toxins, bacteria, and spores that have been largely underexplored to promote a more comprehensive view of this interaction.
Collapse
|
14
|
Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, Antunes A, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H, Mijakovic I, Bajic VB, Lafi FF, Essack M. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters. BMC Genomics 2018; 19:382. [PMID: 29788916 PMCID: PMC5964695 DOI: 10.1186/s12864-018-4796-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. RESULTS We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. CONCLUSIONS B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.
Collapse
Affiliation(s)
- Ghofran Othoum
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Rozaimi Razali
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Ameerah Bokhari
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Soha Alamoudi
- Department of Biology, Science and Arts College, King Abdulaziz University, Rabigh, 21589 Kingdom of Saudi Arabia
| | - André Antunes
- Biology Department, Edge Hill University, L39 4QP, Ormskirk, Lancashire UK
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Heribert Hirt
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Division of Systems & Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Vladimir B. Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Feras F. Lafi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
- Department of Medical Laboratories, Faculty of Health Sciences, American University of Madaba, PO Box 2882, Madaba, Amman JO-11821 Jordan
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| |
Collapse
|
15
|
Felten A, Guillier L, Radomski N, Mistou MY, Lailler R, Cadel-Six S. Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers. PLoS One 2017; 12:e0182082. [PMID: 28750049 PMCID: PMC5531552 DOI: 10.1371/journal.pone.0182082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/12/2017] [Indexed: 11/30/2022] Open
Abstract
Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection) are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes). The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.
Collapse
Affiliation(s)
- Arnaud Felten
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Laurent Guillier
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Nicolas Radomski
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Michel-Yves Mistou
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| |
Collapse
|
16
|
Kovac J, Miller RA, Carroll LM, Kent DJ, Jian J, Beno SM, Wiedmann M. Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade. BMC Genomics 2016; 17:581. [PMID: 27507015 PMCID: PMC4979109 DOI: 10.1186/s12864-016-2883-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus cereus group isolates that produce diarrheal or emetic toxins are frequently isolated from raw milk and, in spore form, can survive pasteurization. Several species within the B. cereus group are closely related and cannot be reliably differentiated by established taxonomical criteria. While B. cereus is traditionally recognized as the principal causative agent of foodborne disease in this group, there is a need to better understand the distribution and expression of different toxin and virulence genes among B. cereus group food isolates to facilitate reliable characterization that allows for assessment of the likelihood of a given isolate to cause a foodborne disease. RESULTS We performed whole genome sequencing of 22 B. cereus group dairy isolates, which represented considerable genetic diversity not covered by other isolates characterized to date. Maximum likelihood analysis of these genomes along with 47 reference genomes representing eight validly published species revealed nine phylogenetic clades. Three of these clades were represented by a single species (B. toyonensis -clade V, B. weihenstephanensis - clade VI, B. cytotoxicus - VII), one by two dairy-associated isolates (clade II; representing a putative new species), one by two species (B. mycoides, B. pseudomycoides - clade I) and four by three species (B. cereus, B. thuringiensis, B. anthracis - clades III-a, b, c and IV). Homologues of genes encoding a principal diarrheal enterotoxin (hemolysin BL) were distributed across all, except the B. cytotoxicus clade. Using a lateral flow immunoassay, hemolysin BL was detected in 13 out of 18 isolates that carried hblACD genes. Isolates from clade III-c (which included B. cereus and B. thuringiensis) consistently did not carry hblACD and did not produce hemolysin BL. Isolates from clade IV (B. cereus, B. thuringiensis) consistently carried hblACD and produced hemolysin BL. Compared to others, clade IV was significantly (p = 0.0001) more likely to produce this toxin. Isolates from clade VI (B. weihenstephanensis) carried hblACD homologues, but did not produce hemolysin BL, possibly due to amino acid substitutions in different toxin-encoding genes. CONCLUSIONS Our results demonstrate that production of diarrheal enterotoxin hemolysin BL is neither inclusive nor exclusive to B. cereus sensu stricto, and that phylogenetic classification of isolates may be better than taxonomic identification for assessment of B. cereus group isolates risk for causing a diarrheal foodborne disease.
Collapse
Affiliation(s)
- Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jiahui Jian
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah M Beno
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|